copick/copick: copick: v2.0.0-alpha.1

2.0.0-alpha.1 (2026-08-18) ⚠ BREAKING CHANGES Newly created tomogram, segmentation, and feature stores are materialized as Zarr v3 groups, and add_features now raises instead of silently retaining existing data when overwrite=False. add_features now resolves the voxel spacing supplied by the caller instead of always using 1.0, so non-1.0 calls write beneath their requested tomogram. Newly written and rebuilt pyramids use OME-Zarr 0.5 metadata and Zarr v3 with numeric level paths; existing Zarr v2 stores remain readable. copick now requires Zarr 3; public .zarr() methods return zarr.abc.store.Store instead of FSStore/MutableMapping, and the removed Zarr 2 copy/store APIs are no longer supported. ✨ Features adopt Zarr 3 runtime while preserving v2 output (#413) (f0aaa39) apply canonical Zarr v3 writer layout (#415) (cf28148), closes #372 canonicalize single-level Zarr exports (#417) (384f132), closes #373 centralize OME-Zarr v2 pyramid writer (#399) (cf3d8bf) drop Python 3.10 support and refresh CI (#412) (fc2c1ef) resolve OME-Zarr levels from metadata (#397) (acc276e) support configurable feature array layouts (#416) (67ecab2) write OME-Zarr 0.5 / Zarr v3 pyramids (#414) (2c56cdb) 🐞 Bug Fixes Bump actions/setup-python from 6 to 7 (#346) (4414023) Bump aiohttp from 3.14.1 to 3.14.2 (#349) (13d5daa) Bump aiohttp from 3.14.2 to 3.14.3 (#396) (c8be04f) Bump black from 26.3.1 to 26.5.1 (#342) (95b6b7b) Bump chanzuckerberg/github-actions from 6.29.4 to 6.30.1 (#340) (d078423) Bump chanzuckerberg/github-actions from 6.30.1 to 6.32.0 (#355) (e085be8) Bump chanzuckerberg/github-actions from 6.32.0 to 6.34.0 (#404) (1f403b9) Bump chanzuckerberg/github-actions from 6.34.0 to 6.36.1 (#422) (aa25ff3) Bump fsspec from 2026.4.0 to 2026.6.0 (#341) (95e23da) Bump mistune from 3.2.1 to 3.3.0 (#338) (6cb895e) Bump numpy from 2.4.2 to 2.4.6 (#423) (2d832fd) Bump pandas from 2.3.3 to 3.0.5 (#427) (b9d650f) Bump pre-commit from 4.6.0 to 4.6.1 (#394) (28c92eb) Bump pre-commit from 4.6.1 to 4.6.2 (#429) (2d26653) Bump pygments from 2.19.2 to 2.20.0 (#407) (3f79dc9) Bump pymdown-extensions from 10.21.3 to 11.0 (#354) (b3ad3cc) Bump ruff from 0.15.20 to 0.15.22 (#350) (864e5f6) Bump ruff from 0.15.22 to 0.16.1 (#405) (dafade9) Bump s3fs from 2026.6.0 to 2026.7.0 (#390) (b0ac9cd) Bump setuptools from 82.0.0 to 83.0.0 (#352) (3eae80b) Bump smbprotocol from 1.16.1 to 1.17.0 (#347) (b3fca95) Bump soupsieve from 2.8.3 to 2.8.4 (#337) (98ab07d) Bump sshfs from 2025.11.0 to 2026.8.0 (#425) (82376f0) Bump textual from 8.2.5 to 8.2.8 (#343) (43cd26b) Bump tqdm from 4.67.3 to 4.68.4 (#344) (7a921ce) Bump tqdm from 4.68.4 to 4.69.0 (#348) (9de66dd) Bump tqdm from 4.69.0 to 4.70.0 (#409) (918ecc0) Bump trimesh from 4.12.2 to 5.0.0 (#391) (b34d701) harden the Zarr v3 cutover and corpus gates (#419) (21fd317) preserve SSH byte-range reads (#434) (1505dd7) ⚡️ Performance Improvements benchmark canonical Zarr v3 I/O tradeoffs (#431) (ddc89bb) 📝 Documentation complete Zarr v3 migration guidance (#436) (ae24715), closes #380 🧪 Tests add Zarr migration structural guards (#402) (0489935) prove Zarr readers remain layout agnostic (#418) (d123754), closes #375 publish the exact Zarr v3 direct-reader fixture (#432) (1f21bf8) validate portal and supported backends (#435) (2612a9f), closes #379 ⚙ Continuous Integration configure v2 alpha releases (ced28a0)